Restarting calculation missmatches

From: Alexandre A. Vakhrouchev (
Date: Thu Jul 19 2007 - 00:59:36 CDT

Hi all!

I calculate water-tube molecular system. Periodic BC and TclBC forces
are used to apply pressure gradient at input of carbone pipe for layer
of 10A along Z-axis. Tube is fixed.
When I restart NAMD job using bincordinates and binvelocities new
calculation is not exact restart of previous results. There is energy
"gap", as an example I attached plot of average velocity of water
molecules along Z-axis.
What is the reason of such phenomena? I use the same force constant.
More over I obsereved the same case without any forces and BC applied.

Thank you in advance!

Dr. Alexandre Vakhrouchev


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